After updating to 17.01 and upon starting Galaxy the Conda package manager will be installed automatically
within the Galaxy’s workspace. This will enable your Galaxy to install tool dependencies from Conda channels
such as BioConda. Such channels are already being used for new and updated tools by IUC
and we suggest adopting this tool dependency resolution method to all tool developers instead of Tool Shed package
recipes - which are now considered deprecated.
Please see the details at the admin documentation

You can now upload compressed (with gzip or bzip2) FASTQ files without them being unpacked automatically (as it was until now).
For this to work you have to select the proper type when uploading (e.g. instead of fastqsanger you select fastqsanger.gz
or fastqsanger.bz2 for compressed files).
Existing tools will work as before and future tools will be able to consume archives and save space in your quota.
Thanks to @abretaud, @ashvark, @jvolkening, and @mvdbeek.
Implemented in Pull Request 3145, `PullRequest 3510`_ and `PullRequest 3514`_.

Previously, Galaxy’s lib directory would be placed on a tool’s PYTHONPATH - but this can cause different sorts of
conflicts with resolved dependencies and should never really have been part of the interface exposed to tools since
it makes both reproducibility and distribution of jobs difficult.

Unfortunately, there is a large number of Galaxy tools - both in the core distribution and in the Tool Shed - that depend on Galaxy internals. The ones we know about have been added to a whitelist as part of Pull Request 3364
and we will continue to add there if we find more. If you discover a tool that has problems importing e.g. galaxy or
galaxy_utils as a result of this release please let us know by creating an issue with a link to the Tool Shed page of the tool.

If you have local tools that depend on these modules and you do not wish to use a formal dependency resolution mechanism
such as Conda, you can change the option preserve_python_environment in galaxy.ini from legacy to legacy_and_local.

Galaxy’s ‘repair repository’ feature for installed repositories is deprecated and will be removed/replaced in the next release - details.